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- PDB-2b3m: Crystal structure of protein AF1124 from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 2b3m
TitleCrystal structure of protein AF1124 from Archaeoglobus fulgidus
Componentshypothetical protein AF1124
KeywordsStructural Genomics / Unknown Function / structural gemonics / Hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
MaoC-like domain-containing protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsChang, C. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of protein AF1124 from Archaeoglobus fulgidus
Authors: Chang, C. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionSep 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein AF1124


Theoretical massNumber of molelcules
Total (without water)17,6321
Polymers17,6321
Non-polymers00
Water2,108117
1
A: hypothetical protein AF1124

A: hypothetical protein AF1124


Theoretical massNumber of molelcules
Total (without water)35,2632
Polymers35,2632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5610 Å2
ΔGint-54 kcal/mol
Surface area13010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.596, 57.596, 142.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein hypothetical protein AF1124


Mass: 17631.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29141
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.2 % / Description: The data includes Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Ammonium Citrate, Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 39206 / Num. obs: 39149 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 47.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3795 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.107 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20534 1096 5.1 %RANDOM
Rwork0.17749 ---
all0.17891 21377 --
obs0.17891 21324 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.739 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 0 117 1324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.981703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66423.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60315239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.313158
X-RAY DIFFRACTIONr_chiral_restr0.10.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02922
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2514
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.2881
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9211.5804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43121269
X-RAY DIFFRACTIONr_scbond_it2.7463516
X-RAY DIFFRACTIONr_scangle_it4.1174.5427
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 66 -
Rwork0.199 1426 -
obs--97.2 %

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